1
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Van den Wouwer B, Brijs K, Carpentier S, Wouters AGB, Raes K. Extractability and chromatographic separation of proteins from potato (Solanum tuberosum L.) trimmings. Food Chem 2024; 450:139301. [PMID: 38613966 DOI: 10.1016/j.foodchem.2024.139301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/26/2024] [Accepted: 04/07/2024] [Indexed: 04/15/2024]
Abstract
By-products from the potato processing industry, like potato trimmings, are sustainable sources of proteins. Here, a size-exclusion high performance liquid chromatography (SE-HPLC) method was applied to simultaneously determine the extractability and aggregation state of proteins from three batches of potato trimmings of different cultivars. Obtained SE-HPLC profiles allowed distinguishing between the patatin and protease inhibitor fractions of potato proteins. Moreover, only 75% of the crude proteins could be extracted in phosphate buffer containing sodium dodecyl sulfate and a reducing agent, indicating the presence of physical extraction barriers. Ball milling for 5 min significantly increased protein extractability, but prolonged treatment resulted in aggregation of native patatin and a reduced protein extractability. Microwave-dried trimmings had a lower protein extractability than freeze-dried trimmings. In future research, the SE-HPLC method can be used to examine changes in potato protein (fractions) as a result of processing.
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Affiliation(s)
- Ben Van den Wouwer
- Research Unit VEG-i-TEC, Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, Sint-Martens-Latemlaan 2B, B-8500 Kortrijk, Belgium; Laboratory of Food Chemistry and Biochemistry, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium.
| | - Kristof Brijs
- Laboratory of Food Chemistry and Biochemistry, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium.
| | - Sebastien Carpentier
- Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Willem de Croylaan 42, B-3001 Leuven, Belgium; SYBIOMA: Facility for Systems Biology Mass Spectrometry, Herestraat 49, B-3000 Leuven, Belgium.
| | - Arno G B Wouters
- Laboratory of Food Chemistry and Biochemistry, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium.
| | - Katleen Raes
- Research Unit VEG-i-TEC, Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, Sint-Martens-Latemlaan 2B, B-8500 Kortrijk, Belgium.
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2
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Stachurska K, Marcisz U, Długosz M, Antosiewicz JM. Kinetics of Structural Transitions Induced by Sodium Dodecyl Sulfate in α-Chymotrypsin. ACS OMEGA 2023; 8:49137-49149. [PMID: 38162786 PMCID: PMC10753550 DOI: 10.1021/acsomega.3c07256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/16/2023] [Accepted: 11/23/2023] [Indexed: 01/03/2024]
Abstract
The temporal changes in circular dichroism at 222 and 260 nm were recorded by using stopped-flow spectroscopy after mixing α-chymotrypsin solutions with sodium dodecyl sulfate solutions. Simultaneously with the circular dichroism signal, the fluorescence emission was recorded. Changes in the secondary and tertiary structures of chymotrypsin induced by sodium dodecyl sulfate are characterized by either three or four one-way reactions with relaxation amplitudes and times precisely determined by an advanced numerical procedure of Kuzmič. Quantitatively, transitions within the secondary and tertiary structures of the protein are significantly different. Moreover, changes in the tertiary structure depend on the type of recorded signal (either circular dichroism or fluorescence) and the wavelength of the incident radiation. The latter observation is particularly interesting as it indicates that the contributions of protein's different tryptophans to the total recorded fluorescence depend on the excitation wavelength. We present several results justifying this hypothesis.
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Affiliation(s)
- Karolina Stachurska
- Biophysics Division, Institute of Experimental
Physics, Faculty of Physics, University
of Warsaw, Pasteura 5 Street, 02-093 Warsaw, Poland
| | - Urszula Marcisz
- Biophysics Division, Institute of Experimental
Physics, Faculty of Physics, University
of Warsaw, Pasteura 5 Street, 02-093 Warsaw, Poland
| | - Maciej Długosz
- Biophysics Division, Institute of Experimental
Physics, Faculty of Physics, University
of Warsaw, Pasteura 5 Street, 02-093 Warsaw, Poland
| | - Jan M. Antosiewicz
- Biophysics Division, Institute of Experimental
Physics, Faculty of Physics, University
of Warsaw, Pasteura 5 Street, 02-093 Warsaw, Poland
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3
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Hartmann A, Sreenivasa K, Schenkel M, Chamachi N, Schake P, Krainer G, Schlierf M. An automated single-molecule FRET platform for high-content, multiwell plate screening of biomolecular conformations and dynamics. Nat Commun 2023; 14:6511. [PMID: 37845199 PMCID: PMC10579363 DOI: 10.1038/s41467-023-42232-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 10/03/2023] [Indexed: 10/18/2023] Open
Abstract
Single-molecule FRET (smFRET) has become a versatile tool for probing the structure and functional dynamics of biomolecular systems, and is extensively used to address questions ranging from biomolecular folding to drug discovery. Confocal smFRET measurements are amongst the widely used smFRET assays and are typically performed in a single-well format. Thus, sampling of many experimental parameters is laborious and time consuming. To address this challenge, we extend here the capabilities of confocal smFRET beyond single-well measurements by integrating a multiwell plate functionality to allow for continuous and automated smFRET measurements. We demonstrate the broad applicability of the multiwell plate assay towards DNA hairpin dynamics, protein folding, competitive and cooperative protein-DNA interactions, and drug-discovery, revealing insights that would be very difficult to achieve with conventional single-well format measurements. For the adaptation into existing instrumentations, we provide a detailed guide and open-source acquisition and analysis software.
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Affiliation(s)
- Andreas Hartmann
- B CUBE Center for Molecular Bioengineering, TU Dresden, Tatzberg 41, 01307, Dresden, Germany.
| | - Koushik Sreenivasa
- B CUBE Center for Molecular Bioengineering, TU Dresden, Tatzberg 41, 01307, Dresden, Germany
- Department of Bionanoscience, Delft University of Technology, 2629HZ, Delft, Netherlands
| | - Mathias Schenkel
- B CUBE Center for Molecular Bioengineering, TU Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Neharika Chamachi
- B CUBE Center for Molecular Bioengineering, TU Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Philipp Schake
- B CUBE Center for Molecular Bioengineering, TU Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Georg Krainer
- B CUBE Center for Molecular Bioengineering, TU Dresden, Tatzberg 41, 01307, Dresden, Germany
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/III, 8010, Graz, Austria
| | - Michael Schlierf
- B CUBE Center for Molecular Bioengineering, TU Dresden, Tatzberg 41, 01307, Dresden, Germany.
- Physics of Life, DFG Cluster of Excellence, TU Dresden, 01062, Dresden, Germany.
- Faculty of Physics, TU Dresden, 01062, Dresden, Germany.
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4
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Chi MC, Lu BY, Huang YF, Wang SW, Lin MG, Wang TF. Effects of Sodium Dodecyl Sulfate on the Enzyme Catalysis and Conformation of a Recombinant γ-Glutamyltranspeptidase from Bacillus licheniformis. Protein J 2023; 42:64-77. [PMID: 36739340 DOI: 10.1007/s10930-023-10095-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2023] [Indexed: 02/06/2023]
Abstract
The study of interactions between proteins and surfactants is of relevance in a diverse range of applications including food, enzymatic detergent formulation, and drug delivery. In spite of sodium dodecyl sulfate (SDS)-induced unfolding has been studied in detail at the protein level, deciphering the conformation-activity relationship of a recombinant γ-glutamyltranspeptidase (BlrGGT) from Bacillus licheniformis remains important to understand how the transpeptidase activity is related to its conformation. In this study, we examined the enzyme catalysis and conformational transition of BlrGGT in the presence of SDS. Enzymatic assays showed that the transpeptidase activity of BlrGGT was greatly affected by SDS in a concentration-dependent manner with approximately 90% inactivation at 6 mM. Native polyacrylamide gel electrophoresis of SDS-treated samples clearly revealed that the heterodimeric enzyme was apparently dissociated into two different subunits at concentrations above 2 mM. The study of enzyme kinetics showed that SDS can act as a mixed-type inhibitor to reduce the catalytic efficiency of BlrGGT. Moreover, the t1/2 value of the enzyme at 55 °C was greatly reduced from 495.1 min to 7.4 min in the presence of 1 mM SDS. The I3/I1 ratio of pyrene excimer fluorescence emission changed around 3.7 mM SDS in the absence of BlrGGT and the inflection point of enzyme samples was reduced to less than 2.7 mM. The Far-UV CD spectrum of the native enzyme had two negative peaks at 208 and 222 nm, respectively; however, both negative peaks increased in magnitude with increasing SDS concentration and reached maximal values at above 4.0 mM. The intrinsic fluorescence spectra of tryptophan further demonstrated that the SDS-induced enzyme conformational transition occurred at approximately 5.1 mM. Tween 20 significantly suppressed the interaction of BlrGGT with SDS by forming mixed micelles at a molar ratio of 1.0. Taken together, this study definitely promotes our better understanding of the relationship between the conformation and catalysis of BlrGGT.
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Affiliation(s)
- Meng-Chun Chi
- Department of Applied Chemistry, National Chiayi University, 300 Syuefu Road, Chiayi City, 60004, Taiwan
| | - Bo-Yuan Lu
- Department of Applied Chemistry, National Chiayi University, 300 Syuefu Road, Chiayi City, 60004, Taiwan
| | - Yu-Fen Huang
- Department of Applied Chemistry, National Chiayi University, 300 Syuefu Road, Chiayi City, 60004, Taiwan
| | - Shih-Wei Wang
- Department of Applied Chemistry, National Chiayi University, 300 Syuefu Road, Chiayi City, 60004, Taiwan
| | - Min-Guan Lin
- Institute of Molecular Biology, Academia Sinica, Nangang District, Taipei City, 11529, Taiwan
| | - Tzu-Fan Wang
- Department of Applied Chemistry, National Chiayi University, 300 Syuefu Road, Chiayi City, 60004, Taiwan.
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5
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David SR, Maheshwaram SK, Shet D, Lakshminarayana MB, Soni GV. Temperature dependent in vitro binding and release of target DNA by Cas9 enzyme. Sci Rep 2022; 12:15243. [PMID: 36085316 PMCID: PMC9463129 DOI: 10.1038/s41598-022-19485-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 08/30/2022] [Indexed: 11/08/2022] Open
Abstract
The CRISPR-associated protein 9 (Cas9) system has proven to be a powerful technology for genome editing in a wide variety of in vivo and in vitro applications. CRISPR-Cas9, when loaded with the guide RNA, cleaves the DNA at the target position as recognized by the guide RNA sequence. For successful application of this technology, it is important to study the biophysical parameters affecting its function. Temperature dependence of the Cas9 binding as well as energetics of product release after cleavage has not been well reported in the literature. In this work, we study the binding properties of Cas9 enzyme to the sequence specific target DNA at a range of temperatures and, surprisingly, find that the Cas9 enzyme, in our study, can find and bind its target DNA with 90 ± 20% efficiency at temperatures as low as 4 °C. Further, we show that the cleaved DNA products remain bound to the Cas9 enzyme strongly and is released from the enzyme only at higher temperatures. Using the gel shift assays, we quantify the rate of Cas9 binding to target DNA to be 0.8 ± 0.2 min-1 at 37 °C. We also tested denaturant (SDS) dependent release of cleaved product which showed a similar release pattern with a dissociation constant of 0.23 ± 0.04 mM. Our results of heat and denaturant dependence on Cas9-DNA binding and release mechanics will provide valuable insights for developing temperature dependent applications of the CRISPR-Cas9 technology.
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Affiliation(s)
| | | | - Divya Shet
- Raman Research Institute, Bangalore, Karnataka, 560080, India
| | | | - Gautam V Soni
- Raman Research Institute, Bangalore, Karnataka, 560080, India.
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6
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Otzen DE, Pedersen JN, Rasmussen HØ, Pedersen JS. How do surfactants unfold and refold proteins? Adv Colloid Interface Sci 2022; 308:102754. [PMID: 36027673 DOI: 10.1016/j.cis.2022.102754] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/25/2022] [Accepted: 08/10/2022] [Indexed: 11/01/2022]
Abstract
Although the anionic surfactant sodium dodecyl sulfate, SDS, has been used for more than half a century as a versatile and efficient protein denaturant for protein separation and size estimation, there is still controversy about its mode of interaction with proteins. The term "rod-like" structures for the complexes that form between SDS and protein, originally introduced by Tanford, is not sufficiently descriptive and does not distinguish between the two current vying models, namely protein-decorated micelles a.k.a. the core-shell model (in which denatured protein covers the surface of micelles) versus beads-on-a-string model (where unfolded proteins are surrounded by surfactant micelles). Thanks to a combination of structural, kinetic and computational work particularly within the last 5-10 years, it is now possible to rule decisively in favor of the core-shell model. This is supported unambiguously by a combination of calorimetric and small-angle X-ray scattering (SAXS) techniques and confirmed by increasingly sophisticated molecular dynamics simulations. Depending on the SDS:protein ratio and the protein molecular mass, the formed structures can range from multiple partly unfolded protein molecules surrounding a single shared micelle to a single polypeptide chain decorating multiple micelles. We also have much new insight into how this species forms. It is preceded by the binding of small numbers of SDS molecules which subsequently grow by accretion. Time-resolved SAXS analysis reveals an asymmetric attack by SDS micelles followed by distribution of the increasingly unfolded protein around the micelle. The compactness of the protein chain continues to evolve at higher SDS concentrations according to single-molecule studies, though the protein remains completely denatured on the tertiary structural level. SDS denaturation can be reversed by addition of nonionic surfactants that absorb SDS forming mixed micelles, leaving the protein free to refold. Refolding can occur in parallel tracks if only a fraction of the protein is initially stripped of SDS. SDS unfolding is nearly always reversible unless carried out at low pH, where charge neutralization can lead to superclusters of protein-surfactant complexes. With the general mechanism of SDS denaturation now firmly established, it largely remains to explore how other ionic surfactants (including biosurfactants) may diverge from this path.
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Affiliation(s)
- Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark; Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, 8000 Aarhus C, Denmark.
| | - Jannik Nedergaard Pedersen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Helena Østergaard Rasmussen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Jan Skov Pedersen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark; Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark.
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7
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Stachurska K, Marcisz U, Długosz M, Antosiewicz JM. Circular Dichroism Spectra of α-Chymotrypsin-SDS Solutions Depend on the Procedure of Their Preparation. ACS OMEGA 2022; 7:23782-23789. [PMID: 35847307 PMCID: PMC9280762 DOI: 10.1021/acsomega.2c02438] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We recorded the far- and near-UV circular dichroism (CD) spectra of solutions of α-chymotrypsin and sodium dodecyl sulfate (SDS) with the final surfactant concentration significantly above the critical micellization concentration. Solutions were prepared using three different procedures. The reference procedure was to mix the chymotrypsin solution with the SDS solution once, immediately achieving the final SDS concentration. In alternative procedures, the protein solutions initially contained some SDS and were mixed with pure SDS solutions at a concentration to provide the same final surfactant as the reference mixing. We demonstrate that the supplementation to the selected final concentration of SDS of the pure chymotrypsin solution leads to different CD spectra than the supplementation to this final concentration of SDS in the chymotrypsin solution containing a small concentration of a few millimolar SDS. These differences disappear when the initial concentration of SDS in the protein solution, which we then supplement to the indicated final concentration, is higher. This suggests the irreversibility of the processes caused by the addition of SDS to chymotrypsin and the influence of the initial amount of this surfactant on the processes occurring with its further addition to the solution. For quantitative analysis of far-UV CD spectra in terms of populations of protein secondary structure elements, we used four well-established software packages. All programs consistently indicate that the observed differences in the far-UV CD spectra can be explained by the differences in the increase in the population of helical forms in chymotrypsin under the influence of SDS.
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8
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Sakuma C, Nakagawa M, Tomioka Y, Maruyama T, Entzminger K, Fleming JK, Shibata T, Kurosawa Y, Okumura CJ, Arakawa T, Akuta T. Western blotting of native proteins from agarose gels. Biotechniques 2022; 72:207-218. [PMID: 35383476 DOI: 10.2144/btn-2022-0012] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We have developed a new Western blotting method of native proteins from agarose-based gel electrophoresis using a buffer at pH 6.1 containing basic histidine and acidic 2-(N-morpholino)ethanesulfonic acid. This gel electrophoresis successfully provided native structures for a variety of proteins and macromolecular complexes. This paper is focused on the Western blotting of native protein bands separated on agarose gels. Two blotting methods from agarose gel to PVDF membrane are introduced here, one by contact (diffusion) blotting and another by electroblotting after pre-treating the agarose gels with SDS. The contact blotting resulted in the transfer of native GFP, native human plexin domain containing protein 2 (PLXDC2) and native SARS-CoV-2 spike protein, which were detected by conformation-specific antibodies generated in-house.
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Affiliation(s)
- Chiaki Sakuma
- Research & Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki, 318-0004, Japan
| | - Masataka Nakagawa
- Research & Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki, 318-0004, Japan
| | - Yui Tomioka
- Research & Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki, 318-0004, Japan
| | - Toshiaki Maruyama
- Abwiz Bio Inc., 9823 Pacific Heights Blvd, suite J, San Diego, CA 9212, USA
| | - Kevin Entzminger
- Abwiz Bio Inc., 9823 Pacific Heights Blvd, suite J, San Diego, CA 9212, USA
| | - Jonathan K Fleming
- Abwiz Bio Inc., 9823 Pacific Heights Blvd, suite J, San Diego, CA 9212, USA
| | - Takashi Shibata
- Research & Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki, 318-0004, Japan
| | - Yasunori Kurosawa
- Research & Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki, 318-0004, Japan.,Abwiz Bio Inc., 9823 Pacific Heights Blvd, suite J, San Diego, CA 9212, USA
| | - C J Okumura
- Abwiz Bio Inc., 9823 Pacific Heights Blvd, suite J, San Diego, CA 9212, USA
| | - Tsutomu Arakawa
- Alliance Protein Laboratories, 13380 Pantera Rd, San Diego, CA 92130, USA
| | - Teruo Akuta
- Research & Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki, 318-0004, Japan
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9
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An Q, Zhang M, Guo D, Wang G, Xu H, Fan C, Li J, Zhang W, Li Y, Chen X, You W, Zhao R. Cr(VI) Removal by Recombinant Escherichia coli Harboring the Main Functional Genes of Sporosarcina saromensis M52. Front Microbiol 2022; 13:820657. [PMID: 35308358 PMCID: PMC8927625 DOI: 10.3389/fmicb.2022.820657] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 02/14/2022] [Indexed: 12/02/2022] Open
Abstract
Hexavalent chromium [Cr(VI)], a recognized heavy metal pollutant, has attracted much attention because of its negative impact on the ecological environment and human health. A chromium-resistant strain, Sporosarcina saromensis M52, was discovered, and the functional genes orf2987, orf3015, orf0415, and orf3237 were identified in the strain by genomics. With the advancement of DNA recombination and gene-splicing technology, genetic engineering technology was used to produce recombinant strains 2987, 3015, 0415, and 3237. The study revealed Cr(VI) tolerance in the order of M52 ≈ 2987 > 3015 ≈ 0415 > 3237 and reduction abilities in the order of M52 ≈ 2987 > 3015 > 0415 ≈ 3237. SEM-EDS, XRD, FT-IR and XPS were utilized to examine the surface structure of the recombinant strains and analyze the surface components and main functional groups. A comprehensive review of the recombinant strains’ capacity to tolerate and reduce Cr(VI) revealed that orf2987 and orf0415 were the main functional genes in Sporosarcina saromensis M52, which may play a key role in removing Cr(VI) and protecting the strain, respectively. The optimum pH for recombinant strains 2987 and 0415 was 7.5–8.5, and the optimum temperature was 37°C. Cu2+ had the greatest promotional effect when Cr(VI) was removed by them, while SDS had an inhibitory effect. This research provided the foundation for further study into the mechanism of Cr(VI) reduction in Sporosarcina saromensis M52, as well as a theoretical basis for the development of effective engineered strains to repair Cr(VI) contamination.
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Affiliation(s)
- Qiuying An
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, China
| | - Min Zhang
- Huzhou Center for Disease Prevention and Control, Huzhou, China
| | - Dongbei Guo
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, China
| | - Guangshun Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, China
| | - Hao Xu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, China
| | - Chun Fan
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, China
| | - Jiayao Li
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Wei Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, China
| | - Yi Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, China
| | - Xiaoxuan Chen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, China
| | - Wanting You
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, China
| | - Ran Zhao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, China
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10
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Mariotti S, Capocefalo A, Chiantore MV, Iacobino A, Teloni R, De Angelis ML, Gallinaro A, Pirillo MF, Borghi M, Canitano A, Michelini Z, Baggieri M, Marchi A, Bucci P, McKay PF, Acchioni C, Sandini S, Sgarbanti M, Tosini F, Di Virgilio A, Venturi G, Marino F, Esposito V, Di Bonito P, Magurano F, Cara A, Negri D, Nisini R. Isolation and Characterization of Mouse Monoclonal Antibodies That Neutralize SARS-CoV-2 and Its Variants of Concern Alpha, Beta, Gamma and Delta by Binding Conformational Epitopes of Glycosylated RBD With High Potency. Front Immunol 2021; 12:750386. [PMID: 34764961 PMCID: PMC8576447 DOI: 10.3389/fimmu.2021.750386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/11/2021] [Indexed: 01/14/2023] Open
Abstract
Antibodies targeting Receptor Binding Domain (RBD) of SARS-CoV-2 have been suggested to account for the majority of neutralizing activity in COVID-19 convalescent sera and several neutralizing antibodies (nAbs) have been isolated, characterized and proposed as emergency therapeutics in the form of monoclonal antibodies (mAbs). However, SARS-CoV-2 variants are rapidly spreading worldwide from the sites of initial identification. The variants of concern (VOC) B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma) and B.1.167.2 (Delta) showed mutations in the SARS-CoV-2 spike protein potentially able to cause escape from nAb responses with a consequent reduction of efficacy of vaccines and mAbs-based therapy. We produced the recombinant RBD (rRBD) of SARS-CoV-2 spike glycoprotein from the Wuhan-Hu 1 reference sequence in a mammalian system, for mice immunization to isolate new mAbs with neutralizing activity. Here we describe four mAbs that were able to bind the rRBD in Enzyme-Linked Immunosorbent Assay and the transmembrane full-length spike protein expressed in HEK293T cells by flow cytometry assay. Moreover, the mAbs recognized the RBD in supernatants of SARS-CoV-2 infected VERO E6 cells by Western Blot under non-reducing condition or in supernatants of cells infected with lentivirus pseudotyped for spike protein, by immunoprecipitation assay. Three out of four mAbs lost their binding efficiency to completely N-deglycosylated rRBD and none was able to bind the same recombinant protein expressed in Escherichia coli, suggesting that the epitopes recognized by three mAbs are generated by the conformational structure of the glycosylated native protein. Of particular relevance, three mAbs were able to inhibit Wuhan SARS-CoV-2 infection of VERO E6 cells in a plaque-reduction neutralization test and the Wuhan SARS-CoV-2 as well as the Alpha, Beta, Gamma and Delta VOC in a pseudoviruses-based neutralization test. These mAbs represent important additional tools for diagnosis and therapy of COVID-19 and may contribute to the understanding of the functional structure of SARS-CoV-2 RBD.
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Affiliation(s)
- Sabrina Mariotti
- Dipartimento di Malattie infettive, Istituto Superiore di Sanità, Roma, Italy
| | - Antonio Capocefalo
- Dipartimento Sicurezza alimentare, nutrizione e sanità pubblica veterinaria, Istituto Superiore di Sanità, Roma, Italy
| | | | - Angelo Iacobino
- Dipartimento di Malattie infettive, Istituto Superiore di Sanità, Roma, Italy
| | - Raffaela Teloni
- Dipartimento di Malattie infettive, Istituto Superiore di Sanità, Roma, Italy
| | - Maria Laura De Angelis
- Dipartimento di Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Roma, Italy
| | - Alessandra Gallinaro
- Centro nazionale per la salute globale, Istituto Superiore di Sanità, Roma, Italy
| | - Maria Franca Pirillo
- Centro nazionale per la salute globale, Istituto Superiore di Sanità, Roma, Italy
| | - Martina Borghi
- Dipartimento di Malattie infettive, Istituto Superiore di Sanità, Roma, Italy
| | - Andrea Canitano
- Centro nazionale per la salute globale, Istituto Superiore di Sanità, Roma, Italy
| | - Zuleika Michelini
- Centro nazionale per la salute globale, Istituto Superiore di Sanità, Roma, Italy
| | - Melissa Baggieri
- Dipartimento di Malattie infettive, Istituto Superiore di Sanità, Roma, Italy
| | - Antonella Marchi
- Dipartimento di Malattie infettive, Istituto Superiore di Sanità, Roma, Italy
| | - Paola Bucci
- Dipartimento di Malattie infettive, Istituto Superiore di Sanità, Roma, Italy
| | - Paul F. McKay
- Department of Infectious Disease, Imperial College, London, United Kingdom
| | - Chiara Acchioni
- Dipartimento di Malattie infettive, Istituto Superiore di Sanità, Roma, Italy
| | - Silvia Sandini
- Dipartimento di Malattie infettive, Istituto Superiore di Sanità, Roma, Italy
| | - Marco Sgarbanti
- Dipartimento di Malattie infettive, Istituto Superiore di Sanità, Roma, Italy
| | - Fabio Tosini
- Dipartimento di Malattie infettive, Istituto Superiore di Sanità, Roma, Italy
| | - Antonio Di Virgilio
- Centro per la sperimentazione ed il benessere animale, Istituto Superiore di Sanità, Roma, Italy
| | - Giulietta Venturi
- Dipartimento di Malattie infettive, Istituto Superiore di Sanità, Roma, Italy
| | - Francesco Marino
- Centro nazionale per il controllo e la valutazione dei farmaci, Istituto Superiore di Sanità, Roma, Italy
| | - Valeria Esposito
- Centro nazionale per il controllo e la valutazione dei farmaci, Istituto Superiore di Sanità, Roma, Italy
| | - Paola Di Bonito
- Dipartimento di Malattie infettive, Istituto Superiore di Sanità, Roma, Italy
| | - Fabio Magurano
- Dipartimento di Malattie infettive, Istituto Superiore di Sanità, Roma, Italy
| | - Andrea Cara
- Centro nazionale per la salute globale, Istituto Superiore di Sanità, Roma, Italy
| | - Donatella Negri
- Dipartimento di Malattie infettive, Istituto Superiore di Sanità, Roma, Italy
| | - Roberto Nisini
- Dipartimento di Malattie infettive, Istituto Superiore di Sanità, Roma, Italy
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11
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Otzen DE, Pedersen JN, Somavarapu AK, Clement A, Ji M, Petersen EH, Pedersen JS, Urban S, Schafer NP. Cys-labeling kinetics of membrane protein GlpG: a role for specific SDS binding and micelle changes? Biophys J 2021; 120:4115-4128. [PMID: 34370995 DOI: 10.1016/j.bpj.2021.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/20/2021] [Accepted: 08/03/2021] [Indexed: 01/01/2023] Open
Abstract
Empirically, α-helical membrane protein folding stability in surfactant micelles can be tuned by varying the mole fraction MFSDS of anionic (sodium dodecyl sulfate (SDS)) relative to nonionic (e.g., dodecyl maltoside (DDM)) surfactant, but we lack a satisfying physical explanation of this phenomenon. Cysteine labeling (CL) has thus far only been used to study the topology of membrane proteins, not their stability or folding behavior. Here, we use CL to investigate membrane protein folding in mixed DDM-SDS micelles. Labeling kinetics of the intramembrane protease GlpG are consistent with simple two-state unfolding-and-exchange rates for seven single-Cys GlpG variants over most of the explored MFSDS range, along with exchange from the native state at low MFSDS (which inconveniently precludes measurement of unfolding kinetics under native conditions). However, for two mutants, labeling rates decline with MFSDS at 0-0.2 MFSDS (i.e., native conditions). Thus, an increase in MFSDS seems to be a protective factor for these two positions, but not for the five others. We propose different scenarios to explain this and find the most plausible ones to involve preferential binding of SDS monomers to the site of CL (based on computational simulations) along with changes in size and shape of the mixed micelle with changing MFSDS (based on SAXS studies). These nonlinear impacts on protein stability highlights a multifaceted role for SDS in membrane protein denaturation, involving both direct interactions of monomeric SDS and changes in micelle size and shape along with the general effects on protein stability of changes in micelle composition.
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Affiliation(s)
- Daniel E Otzen
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus C, Denmark.
| | - Jannik Nedergaard Pedersen
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus C, Denmark
| | - Arun Kumar Somavarapu
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus C, Denmark
| | - Anders Clement
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus C, Denmark
| | - Ming Ji
- Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Emil Hartvig Petersen
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus C, Denmark
| | - Jan Skov Pedersen
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus C, Denmark; Department of Chemistry, Aarhus University, Aarhus C, Denmark
| | - Sinisa Urban
- Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Nicholas P Schafer
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus C, Denmark
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12
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Qiao Y, Luo Y, Long N, Xing Y, Tu J. Single-Molecular Förster Resonance Energy Transfer Measurement on Structures and Interactions of Biomolecules. MICROMACHINES 2021; 12:492. [PMID: 33925350 PMCID: PMC8145425 DOI: 10.3390/mi12050492] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/21/2021] [Accepted: 04/23/2021] [Indexed: 12/15/2022]
Abstract
Single-molecule Förster resonance energy transfer (smFRET) inherits the strategy of measurement from the effective "spectroscopic ruler" FRET and can be utilized to observe molecular behaviors with relatively high throughput at nanometer scale. The simplicity in principle and configuration of smFRET make it easy to apply and couple with other technologies to comprehensively understand single-molecule dynamics in various application scenarios. Despite its widespread application, smFRET is continuously developing and novel studies based on the advanced platforms have been done. Here, we summarize some representative examples of smFRET research of recent years to exhibit the versatility and note typical strategies to further improve the performance of smFRET measurement on different biomolecules.
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Affiliation(s)
- Yi Qiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; (Y.Q.); (Y.L.); (N.L.)
| | - Yuhan Luo
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; (Y.Q.); (Y.L.); (N.L.)
| | - Naiyun Long
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; (Y.Q.); (Y.L.); (N.L.)
| | - Yi Xing
- Institute of Child and Adolescent Health, School of Public Health, Peking University, Beijing 100191, China;
| | - Jing Tu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; (Y.Q.); (Y.L.); (N.L.)
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